WARNING: This e-mail has been altered by MIMEDefang. Following this
paragraph are indications of the actual changes made. For more
information about your site's MIMEDefang policy, contact
Erik Deumens <defang-admin.qtp.ufl.edu>. For more information about MIMEDefang, see:
http://www.roaringpenguin.com/mimedefang/enduser.php3
An attachment named cterm94mod.lib was removed from this document as it
constituted a security hazard. If you require this document, please contact
the sender and arrange an alternate means of receiving it.
An attachment named nterm94mod.lib was removed from this document as it
constituted a security hazard. If you require this document, please contact
the sender and arrange an alternate means of receiving it.
Hi all,
Perhaps someone can advise me on how to persuade sleap to solvate a protein.
Specifically, it's a metalloprotein with some types (N5, N6) for nickel
ions. Tleap handles it just fine. However, in Sleap, I get the following
when it tries to write a prmtop:
[gtkleap]$ saveamberparm model 1FWJ_trimer_high_h2o.prmtop
1FWJ_trimer_high_h2o.rst7
Error: unknown atom type: N5
I'll head off the first obvious question by saying that I have declared
the type N5 in relevant frcmod and prep files, and sleap appears to have
read those files:
(from further up in the sleap STDOUT)
[gtkleap]$ frcmod = loadamberparams 1FWJ_high.frcmod
[gtkleap]$ source 1FWJ_middle.leaprc
loadamberprep 1FWJ_chg2.prep
model = loadpdb 1FWJ_trimer.pdb
I've attached everything used as input to sleap or tleap except the
protein PDB file itself. Furthermore, the STDOUT files for both sleap
and tleap are attached (as sleap.log and tleap.log respectively).
Can anyone shed any light on this problem?
Thanks in advance,
Ben
--
Dr. Benjamin P. Roberts
Postdoctoral Research Associate
Quantum Theory Project
University of Florida
2301 New Physics Building #92
PO Box 118435
Gainesville FL 32611-8435
USA
Phone: +1 352 392 6712
Cell: +1 352 222 3677
Member of the Royal Australian Chemical Institute
and of the American Chemical Society
source leaprc.ff99SB
loadOff cterm94mod.lib
loadOff nterm94mod.lib
# Add atom types
# Why can't these be added automatically by an MCPB script?
addAtomTypes {
{ "HX" "H" "sp3" }
{ "HQ" "H" "sp3" }
{ "N5" "Ni" "sp3" }
{ "N6" "Ni" "sp3" }
{ "NU" "N" "sp2" }
{ "NV" "N" "sp2" }
{ "NW" "N" "sp2" }
{ "NX" "N" "sp2" }
{ "OB" "O" "sp2" }
{ "OK" "O" "sp2" }
{ "OL" "O" "sp2" }
{ "ON" "O" "sp3" }
{ "OO" "O" "sp3" }
{ "OQ" "O" "sp3" }
{ "OU" "O" "sp2" }
}
frcmodMetals = loadamberparams metals.frcmod
1 1 2
1FWJ fragment set created by MTK++/MCPB
Nickel(II) Ion
NI1 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 NI N5 M 3 2 1 1.000 90.000 180.000 1.27465
DONE
Nickel(II) Ion
NI2 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 NI N6 M 3 2 1 1.000 90.000 180.000 0.27155
DONE
ASPARTIC ACID
A21 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.51630
5 H H E 4 3 2 1.010 119.800 0.000 0.29360
6 CA CT M 4 3 2 1.449 121.900 180.000 0.03810
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08800
8 CB CT 3 6 4 3 1.525 111.100 60.000 0.13092
9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.00456
10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.00456
11 CG C B 8 6 4 1.527 109.470 180.000 0.60604
12 OD1 OB E 11 8 6 1.260 117.200 90.000 -0.45860
13 OD2 OU E 11 8 6 1.260 117.200 270.000 -0.65369
14 C C M 6 4 3 1.522 111.100 180.000 0.53660
15 O O E 14 6 4 1.229 120.500 0.000 -0.58190
IMPROPER
-M CA N H
CA +M C O
CB OD1 CG OD2
DONE
HISTIDINE EPSILONH
H11 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600
8 CB CT 3 6 4 3 1.525 111.100 60.000 0.14676
9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02306
10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02306
11 CG CC S 8 6 4 1.510 115.000 180.000 0.13059
12 ND1 NW S 11 8 6 1.390 122.000 180.000 -0.49302
13 CE1 CR B 12 11 8 1.320 108.000 180.000 0.00072
14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.11114
15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.06355
16 HE2 H E 15 13 12 1.010 125.000 180.000 0.30639
17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.25264
18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.22361
19 C C M 6 4 3 1.522 111.100 180.000 0.59730
20 O O E 19 6 4 1.229 120.500 0.000 -0.56790
LOOP
CG CD2
IMPROPER
-M CA N H
CA +M C O
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
DONE
HISTIDINE DELTAH
H12 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CT M 4 3 2 1.449 121.900 180.000 0.01880
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08810
8 CB CT 3 6 4 3 1.525 111.100 60.000 0.08143
9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.00676
10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.00676
11 CG CC S 8 6 4 1.510 115.000 180.000 0.06831
12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.20358
13 HD1 H E 12 11 8 1.010 126.000 0.000 0.38070
14 CE1 CR B 12 11 8 1.320 108.000 180.000 0.14467
15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.06255
16 NE2 NX S 14 12 11 1.310 109.000 0.000 -0.50629
17 CD2 CV S 16 14 12 1.360 110.000 0.000 -0.05762
18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.10469
19 C C M 6 4 3 1.522 111.100 180.000 0.59730
20 O O E 19 6 4 1.229 120.500 0.000 -0.56790
LOOP
CG CD2
IMPROPER
-M CA N H
CA +M C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
DONE
HISTIDINE DELTAH
H21 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CT M 4 3 2 1.449 121.900 180.000 0.01880
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08810
8 CB CT 3 6 4 3 1.525 111.100 60.000 0.03928
9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.01718
10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.01718
11 CG CC S 8 6 4 1.510 115.000 180.000 -0.00577
12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.18614
13 HD1 H E 12 11 8 1.010 126.000 0.000 0.29486
14 CE1 CR B 12 11 8 1.320 108.000 180.000 0.02593
15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.17862
16 NE2 NU S 14 12 11 1.310 109.000 0.000 0.00636
17 CD2 CV S 16 14 12 1.360 110.000 0.000 -0.29529
18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.24205
19 C C M 6 4 3 1.522 111.100 180.000 0.59730
20 O O E 19 6 4 1.229 120.500 0.000 -0.56790
LOOP
CG CD2
IMPROPER
-M CA N H
CA +M C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
DONE
HISTIDINE DELTAH
H22 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CT M 4 3 2 1.449 121.900 180.000 0.01880
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08810
8 CB CT 3 6 4 3 1.525 111.100 60.000 0.01769
9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.06181
10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.06181
11 CG CC S 8 6 4 1.510 115.000 180.000 -0.02373
12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.22596
13 HD1 H E 12 11 8 1.010 126.000 0.000 0.32242
14 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.07437
15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.17627
16 NE2 NV S 14 12 11 1.310 109.000 0.000 -0.09067
17 CD2 CV S 16 14 12 1.360 110.000 0.000 0.02037
18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.03997
19 C C M 6 4 3 1.522 111.100 180.000 0.59730
20 O O E 19 6 4 1.229 120.500 0.000 -0.56790
LOOP
CG CD2
IMPROPER
-M CA N H
CA +M C O
CG CE1 ND1 HD1
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
ND1 CD2 CG CB
DONE
LYSINE NZ-CARBOXYLIC ACID
KCB INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N N M 3 2 1 1.335 116.600 180.000 -0.34790
5 H H E 4 3 2 1.010 119.800 0.000 0.27470
6 CA CT M 4 3 2 1.449 121.900 180.000 -0.24000
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.14260
8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.10064
9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.07462
10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.07462
11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.03603
12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.03394
13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.03394
14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.11262
15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.06026
16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.06026
17 CE CT 3 14 11 8 1.525 109.470 180.000 -0.07196
18 HE2 HC E 17 14 11 1.090 109.500 300.000 0.07319
19 HE3 HC E 17 14 11 1.090 109.500 60.000 0.07319
20 NZ N B 17 14 11 1.470 109.470 180.000 -0.23030
21 HZ1 H E 20 17 14 1.010 120.000 0.000 0.24495
22 CX C B 20 17 14 1.340 120.000 180.000 0.43426
23 OX1 OK E 22 20 17 1.260 117.200 180.000 -0.64076
24 OX2 OL E 22 20 17 1.260 117.200 0.000 -0.48356
25 C C M 6 4 3 1.522 111.100 180.000 0.73410
26 O O E 25 6 4 1.229 120.500 0.000 -0.58940
IMPROPER
-M CA N H
CA +M C O
CE CX NZ HZ1
NZ OX1 CX OX2
DONE
WATER, TIP3P MODEL
ON1 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 H1 HX M 3 2 1 1.000 101.430 -98.890 0.38462
5 O ON M 4 3 2 0.957 104.520 -39.220 -0.67193
6 H2 HX E 5 4 3 0.957 104.520 -151.000 0.38462
DONE
WATER, TIP3P MODEL
ON2 INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 H1 HX M 3 2 1 1.000 101.430 -98.890 0.28631
5 O OO M 4 3 2 0.957 104.520 -39.220 -0.34191
6 H2 HX E 5 4 3 0.957 104.520 -151.000 0.28631
DONE
hydroxyl
ONB INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O OQ M 3 2 1 1.540 111.208 180.000 -1.09258
5 H1 HQ E 4 3 2 0.947 97.223 90.000 0.47786
DONE
STOP
1FWJ parameter set created by MTK++/MCPB
MASS
HQ 1.008
HX 1.008
N5 58.693
N6 58.693
NU 14.010
NV 14.010
NW 14.010
NX 14.010
OB 16.000
OU 16.000
OK 16.000
OL 16.000
ON 16.000
OO 16.000
OQ 16.000
BOND
CB-NU 414.00 1.391
CK-NU 529.00 1.304
CC-NU 410.00 1.394
CR-NU 488.00 1.335
CV-NU 410.00 1.394
LP-NU 600.00 0.200
CB-NV 414.00 1.391
CK-NV 529.00 1.304
CC-NV 410.00 1.394
CR-NV 488.00 1.335
CV-NV 410.00 1.394
LP-NV 600.00 0.200
CB-NW 414.00 1.391
CK-NW 529.00 1.304
CC-NW 410.00 1.394
CR-NW 488.00 1.335
CV-NW 410.00 1.394
LP-NW 600.00 0.200
CB-NX 414.00 1.391
CK-NX 529.00 1.304
CC-NX 410.00 1.394
CR-NX 488.00 1.335
CV-NX 410.00 1.394
LP-NX 600.00 0.200
C -OB 656.00 1.250
OB-P 525.00 1.480
C -OU 656.00 1.250
OU-P 525.00 1.480
C -OK 656.00 1.250
OK-P 525.00 1.480
C -OL 656.00 1.250
OL-P 525.00 1.480
ON-HX 529.58 1.012
OO-HX 529.58 1.012
C -OQ 450.00 1.364
CA-OQ 450.00 1.364
CT-OQ 320.00 1.410
OQ-P 230.00 1.610
HQ-OQ 553.00 0.960
LP-OQ 600.00 0.200
N5-OK 83.45 2.022
N5-NW 60.63 2.149
N5-NX 70.80 2.113
N5-OQ 136.15 1.928
N5-ON 59.88 2.141
N6-NU 67.53 2.127
N6-NV 74.66 2.099
N6-OL 40.79 2.194
N6-OB 107.84 2.087
N6-OQ 107.56 2.042
N6-OO 52.57 2.203
ANGL
C -CB-NU 70.000 130.000
CA-CB-NU 70.000 132.400
CB-CB-NU 70.000 110.400
H5-CK-NU 50.000 123.050
N*-CK-NU 70.000 113.900
CT-CC-NU 70.000 120.000
CW-CC-NU 70.000 120.000
H5-CR-NU 50.000 120.000
NA-CR-NU 70.000 120.000
CC-CV-NU 70.000 120.000
H4-CV-NU 50.000 120.000
CB-NU-CK 70.000 103.800
CC-NU-CR 70.000 117.000
CR-NU-CV 70.000 117.000
CB-NU-LP 50.000 126.000
CC-NU-LP 50.000 126.000
CK-NU-LP 50.000 126.000
CR-NU-LP 50.000 126.000
CV-NU-LP 50.000 126.000
C -CB-NV 70.000 130.000
CA-CB-NV 70.000 132.400
CB-CB-NV 70.000 110.400
H5-CK-NV 50.000 123.050
N*-CK-NV 70.000 113.900
CT-CC-NV 70.000 120.000
CW-CC-NV 70.000 120.000
H5-CR-NV 50.000 120.000
NA-CR-NV 70.000 120.000
CC-CV-NV 70.000 120.000
H4-CV-NV 50.000 120.000
CB-NV-CK 70.000 103.800
CC-NV-CR 70.000 117.000
CR-NV-CV 70.000 117.000
CB-NV-LP 50.000 126.000
CC-NV-LP 50.000 126.000
CK-NV-LP 50.000 126.000
CR-NV-LP 50.000 126.000
CV-NV-LP 50.000 126.000
C -CB-NW 70.000 130.000
CA-CB-NW 70.000 132.400
CB-CB-NW 70.000 110.400
H5-CK-NW 50.000 123.050
N*-CK-NW 70.000 113.900
CT-CC-NW 70.000 120.000
CW-CC-NW 70.000 120.000
H5-CR-NW 50.000 120.000
NA-CR-NW 70.000 120.000
CC-CV-NW 70.000 120.000
H4-CV-NW 50.000 120.000
CB-NW-CK 70.000 103.800
CC-NW-CR 70.000 117.000
CR-NW-CV 70.000 117.000
CB-NW-LP 50.000 126.000
CC-NW-LP 50.000 126.000
CK-NW-LP 50.000 126.000
CR-NW-LP 50.000 126.000
CV-NW-LP 50.000 126.000
C -CB-NX 70.000 130.000
CA-CB-NX 70.000 132.400
CB-CB-NX 70.000 110.400
H5-CK-NX 50.000 123.050
N*-CK-NX 70.000 113.900
CT-CC-NX 70.000 120.000
CW-CC-NX 70.000 120.000
H5-CR-NX 50.000 120.000
NA-CR-NX 70.000 120.000
CC-CV-NX 70.000 120.000
H4-CV-NX 50.000 120.000
CB-NX-CK 70.000 103.800
CC-NX-CR 70.000 117.000
CR-NX-CV 70.000 117.000
CB-NX-LP 50.000 126.000
CC-NX-LP 50.000 126.000
CK-NX-LP 50.000 126.000
CR-NX-LP 50.000 126.000
CV-NX-LP 50.000 126.000
CT-C -OB 70.000 117.000
OB-C -OB 80.000 126.000
OB-P -OH 45.000 108.230
OB-P -OB 40.000 119.900
OB-P -OS 0.000 108.230
CT-C -OU 70.000 117.000
OU-C -OU 80.000 126.000
OU-P -OH 45.000 108.230
OU-P -OU 40.000 119.900
OU-P -OS 0.000 108.230
CT-C -OK 70.000 117.000
OK-C -OK 80.000 126.000
OK-P -OH 45.000 108.230
OK-P -OK 40.000 119.900
OK-P -OS 0.000 108.230
CT-C -OL 70.000 117.000
OL-C -OL 80.000 126.000
OL-P -OH 45.000 108.230
OL-P -OL 40.000 119.900
OL-P -OS 0.000 108.230
HX-ON-HX 37.950 113.240
HX-HX-ON 0.000 33.380
HX-OO-HX 37.950 113.240
HX-HX-OO 0.000 33.380
C -C -OQ 80.000 120.000
CA-C -OQ 70.000 120.000
CT-C -OQ 80.000 110.000
O -C -OQ 80.000 120.000
H4-C -OQ 50.000 120.000
H5-C -OQ 50.000 107.000
CA-CA-OQ 70.000 120.000
HC-CT-N 50.000 109.500
H1-CT-OQ 50.000 109.500
CT-CT-OQ 50.000 109.500
C -OQ-HQ 50.000 113.000
CA-OQ-HQ 50.000 113.000
CT-OQ-HQ 55.000 108.500
HQ-OQ-P 45.000 108.500
O2-P -OQ 45.000 108.230
OQ-P -OS 45.000 102.600
C -OQ-LP 50.000 120.000
CT-OQ-LP 50.000 109.500
HQ-OQ-LP 50.000 109.500
LP-OQ-LP 50.000 109.500
OB-P -OQ 45.000 108.230
OU-P -OQ 45.000 108.230
OK-P -OQ 45.000 108.230
OL-P -OQ 45.000 108.230
NV-N6-OL 43.600 89.630
NV-N6-OB 69.520 90.410
NV-N6-OQ 53.790 165.370
NV-N6-OO 48.890 89.030
OQ-N5-ON 55.740 82.990
OQ-N6-OO 62.890 76.710
NW-N5-NX 61.420 90.100
NW-N5-OQ 41.300 153.900
NW-N5-ON 60.350 87.550
OK-N5-NW 57.250 100.820
OK-N5-NX 56.140 98.610
OK-N5-OQ 31.310 103.610
OK-N5-ON 53.150 91.080
OK-C -OL 121.980 125.340
N -C -OK 126.780 117.860
N -C -OL 130.620 116.740
NU-N6-NV 51.570 93.090
NU-N6-OL 53.170 92.420
NU-N6-OB 54.520 93.410
NU-N6-OQ 62.910 101.420
NU-N6-OO 50.670 173.860
N5-OK-C 85.190 119.160
N5-NW-CC 98.530 132.820
N5-NW-CR 93.900 120.060
N5-NX-CV 75.690 128.870
N5-NX-CR 75.950 124.520
N5-OQ-N6 77.280 122.680
N5-OQ-HQ 34.810 122.260
N5-ON-HX 35.320 104.600
OB-N6-OQ 67.000 90.540
OB-N6-OO 49.980 80.800
OB-C -OU 140.260 125.550
OL-N6-OB 50.490 174.160
OL-N6-OQ 34.520 87.950
OL-N6-OO 50.110 93.360
N6-NU-CV 71.790 128.370
N6-NU-CR 71.600 124.900
N6-NV-CV 76.590 126.760
N6-NV-CR 75.380 125.860
N6-OL-C 68.610 118.740
N6-OB-C 99.840 124.880
N6-OQ-HQ 36.010 99.450
N6-OO-HX 22.150 87.200
NX-N5-OQ 51.720 95.160
NX-N5-ON 55.100 170.300
DIHE
X -CB-NU-X 2 5.100 180.000 2.000
X -CC-NU-X 2 4.800 180.000 2.000
X -CK-NU-X 2 20.000 180.000 2.000
X -CR-NU-X 2 10.000 180.000 2.000
X -CV-NU-X 2 4.800 180.000 2.000
X -CB-NV-X 2 5.100 180.000 2.000
X -CC-NV-X 2 4.800 180.000 2.000
X -CK-NV-X 2 20.000 180.000 2.000
X -CR-NV-X 2 10.000 180.000 2.000
X -CV-NV-X 2 4.800 180.000 2.000
X -CB-NW-X 2 5.100 180.000 2.000
X -CC-NW-X 2 4.800 180.000 2.000
X -CK-NW-X 2 20.000 180.000 2.000
X -CR-NW-X 2 10.000 180.000 2.000
X -CV-NW-X 2 4.800 180.000 2.000
X -CB-NX-X 2 5.100 180.000 2.000
X -CC-NX-X 2 4.800 180.000 2.000
X -CK-NX-X 2 20.000 180.000 2.000
X -CR-NX-X 2 10.000 180.000 2.000
X -CV-NX-X 2 4.800 180.000 2.000
X -C -OQ-X 2 4.600 180.000 2.000
X -CA-OQ-X 2 1.800 180.000 2.000
X -CT-OQ-X 3 0.500 0.000 3.000
X -OQ-P -X 3 0.750 0.000 3.000
OQ-P -OS-CT 1 0.250 0.000 -3.000
OQ-P -OS-CT 1 1.200 0.000 2.000
HQ-OQ-CT-CT 1 0.160 0.000 -3.000
HQ-OQ-CT-CT 1 0.250 0.000 1.000
HQ-OQ-C -O 1 2.300 180.000 -2.000
HQ-OQ-C -O 1 1.900 0.000 1.000
OS-CT-CT-OQ 1 0.144 0.000 -3.000
OS-CT-CT-OQ 1 1.175 0.000 2.000
OQ-CT-CT-OQ 1 0.144 0.000 -3.000
OQ-CT-CT-OQ 1 1.175 0.000 2.000
H1-CT-CT-OQ 1 0.000 0.000 -3.000
H1-CT-CT-OQ 1 0.250 0.000 1.000
HC-CT-CT-OQ 1 0.000 0.000 -3.000
HC-CT-CT-OQ 1 0.250 0.000 1.000
H1-CT-OQ-LP 1 0.000 0.000 3.000
CT-CT-OQ-LP 1 0.000 0.000 3.000
OQ-N5-ON-HX 3 0.000 0.000 3.000
N6-OO-HX-HX 3 0.000 0.000 3.000
OB-N6-OQ-HQ 3 0.000 0.000 3.000
OB-N6-OO-HX 3 0.000 0.000 3.000
C -OL-N6-OB 3 0.000 0.000 3.000
C -OL-N6-OQ 3 0.000 0.000 3.000
C -OL-N6-OO 3 0.000 0.000 3.000
NU-N6-NV-CV 3 0.000 0.000 3.000
NU-N6-NV-CR 3 0.000 0.000 3.000
NU-N6-OL-C 3 0.000 0.000 3.000
NU-N6-OB-C 3 0.000 0.000 3.000
NU-N6-OQ-HQ 3 0.000 0.000 3.000
NU-N6-OO-HX 3 0.000 0.000 3.000
CV-NU-N6-NV 3 0.000 0.000 3.000
CV-NU-N6-OL 3 0.000 0.000 3.000
CV-NU-N6-OB 3 0.000 0.000 3.000
CV-NU-N6-OQ 3 0.000 0.000 3.000
CV-NU-N6-OO 3 0.000 0.000 3.000
C -OB-N6-OQ 3 0.000 0.000 3.000
C -OB-N6-OO 3 0.000 0.000 3.000
CR-NV-N6-OL 3 0.000 0.000 3.000
CR-NV-N6-OB 3 0.000 0.000 3.000
CR-NV-N6-OQ 3 0.000 0.000 3.000
CR-NV-N6-OO 3 0.000 0.000 3.000
CR-NW-N5-NX 3 0.000 0.000 3.000
CR-NW-N5-OQ 3 0.000 0.000 3.000
CR-NW-N5-ON 3 0.000 0.000 3.000
NV-N6-OL-C 3 0.000 0.000 3.000
NV-N6-OB-C 3 0.000 0.000 3.000
NV-N6-OQ-HQ 3 0.000 0.000 3.000
NV-N6-OO-HX 3 0.000 0.000 3.000
CV-NX-N5-OQ 3 0.000 0.000 3.000
CV-NX-N5-ON 3 0.000 0.000 3.000
OQ-N6-OO-HX 3 0.000 0.000 3.000
N6-OQ-N5-OK 3 0.000 0.000 3.000
N6-OQ-N5-NW 3 0.000 0.000 3.000
N6-OQ-N5-NX 3 0.000 0.000 3.000
N6-OQ-N5-ON 3 0.000 0.000 3.000
N5-ON-HX-HX 3 0.000 0.000 3.000
NW-N5-NX-CV 3 0.000 0.000 3.000
NW-N5-NX-CR 3 0.000 0.000 3.000
NW-N5-OQ-HQ 3 0.000 0.000 3.000
NW-N5-ON-HX 3 0.000 0.000 3.000
NX-N5-OQ-HQ 3 0.000 0.000 3.000
NX-N5-ON-HX 3 0.000 0.000 3.000
CR-NU-N6-NV 3 0.000 0.000 3.000
CR-NU-N6-OL 3 0.000 0.000 3.000
CR-NU-N6-OB 3 0.000 0.000 3.000
CR-NU-N6-OQ 3 0.000 0.000 3.000
CR-NU-N6-OO 3 0.000 0.000 3.000
HQ-OQ-N5-ON 3 0.000 0.000 3.000
HQ-OQ-N6-OO 3 0.000 0.000 3.000
OL-N6-OB-C 3 0.000 0.000 3.000
OL-N6-OQ-HQ 3 0.000 0.000 3.000
OL-N6-OO-HX 3 0.000 0.000 3.000
OK-N5-NW-CC 3 0.000 0.000 3.000
OK-N5-NW-CR 3 0.000 0.000 3.000
OK-N5-NX-CV 3 0.000 0.000 3.000
OK-N5-NX-CR 3 0.000 0.000 3.000
OK-N5-OQ-HQ 3 0.000 0.000 3.000
OK-N5-ON-HX 3 0.000 0.000 3.000
CR-NX-N5-OQ 3 0.000 0.000 3.000
CR-NX-N5-ON 3 0.000 0.000 3.000
CC-NW-N5-NX 3 0.000 0.000 3.000
CC-NW-N5-OQ 3 0.000 0.000 3.000
CC-NW-N5-ON 3 0.000 0.000 3.000
C -OK-N5-NW 3 0.000 0.000 3.000
C -OK-N5-NX 3 0.000 0.000 3.000
C -OK-N5-OQ 3 0.000 0.000 3.000
C -OK-N5-ON 3 0.000 0.000 3.000
N6-OB-C -CT 3 0.000 0.000 3.000
N6-OB-C -OU 3 0.000 0.000 3.000
N5-OQ-N6-NU 3 0.000 0.000 3.000
N5-OQ-N6-NV 3 0.000 0.000 3.000
N5-OQ-N6-OL 3 0.000 0.000 3.000
N5-OQ-N6-OB 3 0.000 0.000 3.000
N5-OQ-N6-OO 3 0.000 0.000 3.000
N6-OL-C -N 3 0.000 0.000 3.000
N6-OL-C -OK 3 0.000 0.000 3.000
N5-OK-C -N 3 0.000 0.000 3.000
N5-OK-C -OL 3 0.000 0.000 3.000
CV-NV-N6-OL 3 0.000 0.000 3.000
CV-NV-N6-OB 3 0.000 0.000 3.000
CV-NV-N6-OQ 3 0.000 0.000 3.000
CV-NV-N6-OO 3 0.000 0.000 3.000
IMPR
CT-CW-CC-NU 1.100 180.000 2.000
CT-CW-CC-NV 1.100 180.000 2.000
CT-CW-CC-NW 1.100 180.000 2.000
CT-CW-CC-NX 1.100 180.000 2.000
X -OB-C -OB 10.500 180.000 2.000
X -OU-C -OU 10.500 180.000 2.000
X -OK-C -OK 10.500 180.000 2.000
X -OL-C -OL 10.500 180.000 2.000
CT-O -C -OQ 10.500 180.000 2.000
CA-CA-C -OQ 1.100 180.000 2.000
CA-CA-CA-OQ 1.100 180.000 2.000
H5-O -C -OQ 1.100 180.000 2.000
NONB
HQ 0.60 0.0157
HX 0.60 0.0157
N5 0.00 0.000
N6 0.00 0.000
NU 1.82 0.170
NV 1.82 0.170
NW 1.82 0.170
NX 1.82 0.170
OB 1.66 0.210
OU 1.66 0.210
OK 1.66 0.210
OL 1.66 0.210
ON 1.78 0.155
OO 1.78 0.155
OQ 1.72 0.210
source 1FWJ_beginning.leaprc
frcmod = loadamberparams 1FWJ_high.frcmod
source 1FWJ_middle.leaprc
saveamberparm model 1FWJ_trimer_high_h2o.prmtop 1FWJ_trimer_high_h2o.rst7
savePdb model 1FWJ_trimer_high_h2o.pdb
quit
loadamberprep 1FWJ_chg2.prep
model = loadpdb 1FWJ_trimer.pdb
bond model.1.NI model.419.OX1
bond model.1.NI model.448.ND1
bond model.1.NI model.474.NE2
bond model.1.NI model.770.O
bond model.1.NI model.771.O
bond model.2.NI model.336.NE2
bond model.2.NI model.338.NE2
bond model.2.NI model.419.OX2
bond model.2.NI model.562.OD1
bond model.2.NI model.770.O
bond model.2.NI model.772.O
bond model.773.NI model.1191.OX1
bond model.773.NI model.1220.ND1
bond model.773.NI model.1246.NE2
bond model.773.NI model.1542.O
bond model.773.NI model.1543.O
bond model.774.NI model.1108.NE2
bond model.774.NI model.1110.NE2
bond model.774.NI model.1191.OX2
bond model.774.NI model.1334.OD1
bond model.774.NI model.1542.O
bond model.774.NI model.1544.O
bond model.1545.NI model.1963.OX1
bond model.1545.NI model.1992.ND1
bond model.1545.NI model.2018.NE2
bond model.1545.NI model.2314.O
bond model.1545.NI model.2315.O
bond model.1546.NI model.1880.NE2
bond model.1546.NI model.1882.NE2
bond model.1546.NI model.1963.OX2
bond model.1546.NI model.2106.OD1
bond model.1546.NI model.2314.O
bond model.1546.NI model.2316.O
solvateOct model TIP3PBOX 20.0 iso
#addIons model Na+ 239 Cl- 167
metals parameter set created by MTK++/MCPB
MASS
FE 55.845
CO 58.933
NI 58.693
U1 63.550
CU 63.550
ZN 65.400
RU 101.070
BOND
ANGL
DIHE
IMPR
NONB
FE 0.00 0.000
CO 0.00 0.000
NI 0.00 0.000
U1 1.20 0.050
CU 1.20 0.050
ZN 1.10 0.013
RU 1.10 0.013
[gtkleap]$ source 1FWJ_beginning.leaprc
source leaprc.ff99SB
logFile leap.log
#
# ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
# ----- this file is updated for PDB format 3
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "C2" "C" "sp3" }
{ "C3" "C" "sp3" }
{ "C" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "CE" "C" "sp2" }
{ "CF" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp2" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "C" "sp2" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "F" "F" "sp3" }
{ "CL" "Cl" "sp3" }
{ "BR" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "FE" "Fe" "sp3" }
{ "EP" "" "sp3" }
# glycam
{ "OG" "O" "sp3" }
{ "OL" "O" "sp3" }
{ "AC" "C" "sp3" }
{ "EC" "C" "sp3" }
}
#
# Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
#
# Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
# Load main chain and terminating
# amino acid libraries (i.e. ff94 libs)
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
#
# Load water and ions
#
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
# Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
{ 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" }
{ 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" }
{ 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" }
{ 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" }
{ 0 "DG" "DG5" } { 1 "DG" "DG3" }
{ 0 "DA" "DA5" } { 1 "DA" "DA3" }
{ 0 "DC" "DC5" } { 1 "DC" "DC3" }
{ 0 "DT" "DT5" } { 1 "DT" "DT3" }
}
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "O2*" "O2'" }
{ "H1*" "H1'" }
{ "H2*1" "H2'1" }
{ "H2*2" "H2'2" }
{ "H2'" "H2'1" }
{ "H2''" "H2'2" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'1" }
{ "H5*2" "H5'2" }
{ "H5'" "H5'1" }
{ "H5''" "H5'2" }
{ "HO2'" "HO'2" }
{ "HO5'" "H5T" }
{ "HO3'" "H3T" }
{ "O1'" "O4'" }
{ "OA" "O1P" }
{ "OB" "O2P" }
{ "OP1" "O1P" }
{ "OP2" "O2P" }
}
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
loadOff cterm94mod.lib
loadOff nterm94mod.lib
# Add atom types
# Why can't these be added automatically by an MCPB script?
addAtomTypes {
{ "HX" "H" "sp3" }
{ "HQ" "H" "sp3" }
{ "N5" "Ni" "sp3" }
{ "N6" "Ni" "sp3" }
{ "NU" "N" "sp2" }
{ "NV" "N" "sp2" }
{ "NW" "N" "sp2" }
{ "NX" "N" "sp2" }
{ "OB" "O" "sp2" }
{ "OK" "O" "sp2" }
{ "OL" "O" "sp2" }
{ "ON" "O" "sp3" }
{ "OO" "O" "sp3" }
{ "OQ" "O" "sp3" }
{ "OU" "O" "sp2" }
}
frcmodMetals = loadamberparams metals.frcmod
[gtkleap]$ frcmod = loadamberparams 1FWJ_high.frcmod
[gtkleap]$ source 1FWJ_middle.leaprc
loadamberprep 1FWJ_chg2.prep
model = loadpdb 1FWJ_trimer.pdb
bond model.1.NI model.419.OX1
bond model.1.NI model.448.ND1
bond model.1.NI model.474.NE2
bond model.1.NI model.770.O
bond model.1.NI model.771.O
bond model.2.NI model.336.NE2
bond model.2.NI model.338.NE2
bond model.2.NI model.419.OX2
bond model.2.NI model.562.OD1
bond model.2.NI model.770.O
bond model.2.NI model.772.O
bond model.773.NI model.1191.OX1
bond model.773.NI model.1220.ND1
bond model.773.NI model.1246.NE2
bond model.773.NI model.1542.O
bond model.773.NI model.1543.O
bond model.774.NI model.1108.NE2
bond model.774.NI model.1110.NE2
bond model.774.NI model.1191.OX2
bond model.774.NI model.1334.OD1
bond model.774.NI model.1542.O
bond model.774.NI model.1544.O
bond model.1545.NI model.1963.OX1
bond model.1545.NI model.1992.ND1
bond model.1545.NI model.2018.NE2
bond model.1545.NI model.2314.O
bond model.1545.NI model.2315.O
bond model.1546.NI model.1880.NE2
bond model.1546.NI model.1882.NE2
bond model.1546.NI model.1963.OX2
bond model.1546.NI model.2106.OD1
bond model.1546.NI model.2314.O
bond model.1546.NI model.2316.O
solvateOct model TIP3PBOX 20.0 iso
rgn size: 173.354 173.354 173.354
svt size: 18.774 18.774 18.774
nx,ny,nz: 10 10 10
#addIons model Na+ 239 Cl- 167
[gtkleap]$ saveamberparm model 1FWJ_trimer_high_h2o.prmtop 1FWJ_trimer_high_h2o.rst7
Error: unknown atom type: N5
-I: Adding /Applications/Amber11/intel-mkl/dat/leap/prep to search path.
-I: Adding /Applications/Amber11/intel-mkl/dat/leap/lib to search path.
-I: Adding /Applications/Amber11/intel-mkl/dat/leap/parm to search path.
-I: Adding /Applications/Amber11/intel-mkl/dat/leap/cmd to search path.
-f: Source 1FWJ_high.leaprc.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./1FWJ_high.leaprc
----- Source: ./1FWJ_beginning.leaprc
----- Source of ./1FWJ_beginning.leaprc done
----- Source: /Applications/Amber11/intel-mkl/dat/leap/cmd/leaprc.ff99SB
----- Source of /Applications/Amber11/intel-mkl/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /Applications/Amber11/intel-mkl/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /Applications/Amber11/intel-mkl/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /Applications/Amber11/intel-mkl/dat/leap/lib/all_nucleic94.lib
Loading library: /Applications/Amber11/intel-mkl/dat/leap/lib/all_amino94.lib
Loading library: /Applications/Amber11/intel-mkl/dat/leap/lib/all_aminoct94.lib
Loading library: /Applications/Amber11/intel-mkl/dat/leap/lib/all_aminont94.lib
Loading library: /Applications/Amber11/intel-mkl/dat/leap/lib/ions94.lib
Loading library: /Applications/Amber11/intel-mkl/dat/leap/lib/solvents.lib
Loading library: ./cterm94mod.lib
Loading library: ./nterm94mod.lib
Loading parameters: ./metals.frcmod
Reading force field modification type file (frcmod)
Reading title:
metals parameter set created by MTK++/MCPB
Loading parameters: ./1FWJ_high.frcmod
Reading force field modification type file (frcmod)
Reading title:
1FWJ parameter set created by MTK++/MCPB
----- Source: ./1FWJ_middle.leaprc
----- Source of ./1FWJ_middle.leaprc done
Loading Prep file: ./1FWJ_chg2.prep
Loading PDB file: ./1FWJ_trimer.pdb
total atoms in file: 34686
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
Scaling up box by a factor of 1.312602 to meet diagonal cut criterion
Solute vdw bounding box: 69.904 120.030 120.808
Total bounding box for atom centers: 173.312 173.312 173.312
(box expansion for 'iso' is 42.2%)
Solvent unit box: 18.774 18.774 18.774
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
(using default radius 1.500000 for NI)
Volume: 2648212.721 A^3 (oct)
Total mass 1507439.866 amu, Density 0.945 g/cc
Added 69925 residues.
Checking Unit.
WARNING: The unperturbed charge of the unit: -72.000060 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<H21 336>: -M CA N H
<H21 336>: CA +M C O
<H21 336>: CG CE1 ND1 HD1
<H21 336>: CG NE2 CD2 HD2
<H21 336>: ND1 NE2 CE1 HE1
<H21 336>: ND1 CD2 CG CB
<H22 338>: -M CA N H
<H22 338>: CA +M C O
<H22 338>: CG CE1 ND1 HD1
<H22 338>: CG NE2 CD2 HD2
<H22 338>: ND1 NE2 CE1 HE1
<H22 338>: ND1 CD2 CG CB
<KCB 419>: -M CA N H
<KCB 419>: CA +M C O
<KCB 419>: CE CX NZ HZ1
<KCB 419>: NZ OX1 CX OX2
<H11 448>: -M CA N H
<H11 448>: CA +M C O
<H11 448>: CE1 CD2 NE2 HE2
<H11 448>: CG NE2 CD2 HD2
<H11 448>: ND1 NE2 CE1 HE1
<H11 448>: ND1 CD2 CG CB
<H12 474>: -M CA N H
<H12 474>: CA +M C O
<H12 474>: CG CE1 ND1 HD1
<H12 474>: CG NE2 CD2 HD2
<H12 474>: ND1 NE2 CE1 HE1
<H12 474>: ND1 CD2 CG CB
<A21 562>: -M CA N H
<A21 562>: CA +M C O
<A21 562>: CB OD1 CG OD2
<H21 1108>: -M CA N H
<H21 1108>: CA +M C O
<H21 1108>: CG CE1 ND1 HD1
<H21 1108>: CG NE2 CD2 HD2
<H21 1108>: ND1 NE2 CE1 HE1
<H21 1108>: ND1 CD2 CG CB
<H22 1110>: -M CA N H
<H22 1110>: CA +M C O
<H22 1110>: CG CE1 ND1 HD1
<H22 1110>: CG NE2 CD2 HD2
<H22 1110>: ND1 NE2 CE1 HE1
<H22 1110>: ND1 CD2 CG CB
<KCB 1191>: -M CA N H
<KCB 1191>: CA +M C O
<KCB 1191>: CE CX NZ HZ1
<KCB 1191>: NZ OX1 CX OX2
<H11 1220>: -M CA N H
<H11 1220>: CA +M C O
<H11 1220>: CE1 CD2 NE2 HE2
<H11 1220>: CG NE2 CD2 HD2
<H11 1220>: ND1 NE2 CE1 HE1
<H11 1220>: ND1 CD2 CG CB
<H12 1246>: -M CA N H
<H12 1246>: CA +M C O
<H12 1246>: CG CE1 ND1 HD1
<H12 1246>: CG NE2 CD2 HD2
<H12 1246>: ND1 NE2 CE1 HE1
<H12 1246>: ND1 CD2 CG CB
<A21 1334>: -M CA N H
<A21 1334>: CA +M C O
<A21 1334>: CB OD1 CG OD2
<H21 1880>: -M CA N H
<H21 1880>: CA +M C O
<H21 1880>: CG CE1 ND1 HD1
<H21 1880>: CG NE2 CD2 HD2
<H21 1880>: ND1 NE2 CE1 HE1
<H21 1880>: ND1 CD2 CG CB
<H22 1882>: -M CA N H
<H22 1882>: CA +M C O
<H22 1882>: CG CE1 ND1 HD1
<H22 1882>: CG NE2 CD2 HD2
<H22 1882>: ND1 NE2 CE1 HE1
<H22 1882>: ND1 CD2 CG CB
<KCB 1963>: -M CA N H
<KCB 1963>: CA +M C O
<KCB 1963>: CE CX NZ HZ1
<KCB 1963>: NZ OX1 CX OX2
<H11 1992>: -M CA N H
<H11 1992>: CA +M C O
<H11 1992>: CE1 CD2 NE2 HE2
<H11 1992>: CG NE2 CD2 HD2
<H11 1992>: ND1 NE2 CE1 HE1
<H11 1992>: ND1 CD2 CG CB
<H12 2018>: -M CA N H
<H12 2018>: CA +M C O
<H12 2018>: CG CE1 ND1 HD1
<H12 2018>: CG NE2 CD2 HD2
<H12 2018>: ND1 NE2 CE1 HE1
<H12 2018>: ND1 CD2 CG CB
<A21 2106>: -M CA N H
<A21 2106>: CA +M C O
<A21 2106>: CB OD1 CG OD2
total 6780 improper torsions applied
93 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
ILC 3
LEC 3
MEN 6
PHC 3
SEN 3
WAT 69925
)
(no restraints)
Writing pdb file: 1FWJ_trimer_high_h2o.pdb
Quit
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 01 2010 - 07:30:02 PST
